You are a walking – or running – bacteria colony. There are around 100 trillion microbes, mostly bacteria, living in and on your body, the majority in your large intestine. Bacteria outnumber your own body cells by about 10:1. And their genes outnumber your genes by over 100:1. Collectively, they form your microbiome. But what, exactly, have they got to do with running?

Quite a lot, surprisingly, because these microbes in your gut are not only essential to your ability to digest food, but they also provide vital nutrients and enzymes, and are involved in metabolism. They can alter the way you store fat, how you balance your blood glucose levels and how you respond to hormones signalling hunger and satiety. Your microbiome also protects you against pathogens (agents of disease), controls hormones and trains your immune system. (In fact, your gut has the largest number of immune cells and the largest number of hormone cells in the body). And, crucially, you can influence how well it does these things.

Everyone’s microbiome is unique, like a fingerprint. We pick up our mother’s microbiome during birth. Then, as we go through life, it’s in flux, moderated by diet, lifestyle, stress, medication, exercise and even factors such as exposure to animals and dirt.

Only in the past decade have we had the knowledge and technology – rapid gene-sequencing techniques – to identify different strains of bacteria and what their function might be. We know if your microbiome is out of balance then digestive and weight issues, low mood and low immunity can result. While it’s unlikely to be a straightforward cause-and-effect situation, research has also found links between poor gut flora and irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), obesity, type 2 diabetes, Parkinson’s disease, Alzheimer’s disease, arthritis, cardiovascular disease, colon cancer, depression, anxiety, autism, asthma, allergies and respiratory tract infections (RTIs).

‘The real secret to how our bodies respond to different foods lies in our microbes, not our genes, as was always thought,’ says Tim Spector, professor of genetic epidemiology at King’s College London and author of The Diet Myth. ‘It’s why some people store carbs as fat more easily than others, why some runners do better on a high-protein diet or why some are predisposed to obesity. As we come to understand the complexities of this, we can do a lot more to tailor our diets and improve all aspects of our health.’

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Can bacteria boost my running?

‘A lot of runners come to see me because they’re not getting the results they want but can’t work out why,’ says Sarah Danaher, a clinical and sports dietitian based in Northern Ireland. ‘And one of the first things we’ll do is work on boosting their microbiome.’ Danaher is not alone in taking this approach; the expert consensus is that the right balance of gut flora can improve running performance. The exact mechanisms are yet to be fully understood, but it’s likely we’re looking at a host of indirect effects that equal a performance benefit.

Research at National Taiwan Sport University, published in the Journal of Strength and Conditioning Research, looked at the effect of gut microbes on exercise performance in mice. The study found those with normal gut bacteria fared better in a time-to-exhaustion swimming test, while those sterilised to have no gut bacteria performed the worst. The researchers suggest metabolism and antioxidant response may be key.

Last year, a large review by scientists at Shanghai University of Sport, published in the Journal of Sport and Health Science, looked to identify more closely the relationship between endurance exercise and the microbiome, particularly at what role a healthy microbiome might play in adaptations to exercise. The review looked at 33 papers published since 2007 and concluded that the microbiome may play a key role in controlling oxidative stress and inflammatory responses, as well as improving energy expenditure, hydration and metabolism during intense exercise.

‘We know a healthy microbiome has a positive effect on immunity and inflammation, as well as energy release,’ says Spector. ‘This will benefit the runner in both the short and long term, contributing to a better run as well as improved recovery and faster fitness gains.’

With better immunity, runners are also less likely to suffer from respiratory tract infections, as well as tummy bugs and other GI problems that can trash our training.

What about the other ‘runs’?

While we runners spend plenty of time thinking about the digestive perils of our sport, like those dreaded midrun bowel rebellions, research suggests that in the longer term exercise can produce a healthier, more diverse microbiome and, with this, all the knock-on effects on not just digestion but also mood, immunity, chronic disease risk and more.

A recent study published in the journal Gut, which compared 40 professional athletes with ordinary, healthy men, found that the athletes had a significantly higher diversity of gut microbes, including bacteria associated with lower rates of obesity and obesity-related disorders. This provides evidence for the effect of exercise on the microbiome – although, as Spector points out, the relationship was likely to be complex and influenced by the healthy diets followed by elite sportspeople.

Other studies in Spain and at the University of Colorado in the US have found increasing moderate-exercise frequency in humans has a beneficial effect on gut bacteria, increasing diversity of beneficial strains. Similar results have been found in rat and mice studies.

‘We don’t know enough yet to prescribe certain types of exercise; suffice to say that there’s an all-round benefit to being active,’ says Spector. And it’s a two-way street: run to boost your microbiome, boost your microbiome to improve your adaptation to running.

That may not sit comfortably with runners who find themselves doubled up with cramps during or after a run, or who spend the hours before a race in the queue for the portable toilets. But building a better microbiome is the best approach to these gut gripes, too – whatever their cause. ‘Runners are known for gastrointestinal issues, particularly those that push themselves harder for distance or times,’ says Professor Peter Whorwell, consultant gastroenterologist and author of Take Control of Your IBS. ‘Marathoners often complain of loose bowels, not just when running, but all the time. It’s often the case that they have irritable bowel syndrome (IBS), perhaps without knowing, and vigorous exercise makes it worse.’

IBS is a tricky condition for runners, as stress is also a common trigger. ‘So if going for a run de-stresses you, then it can be a helpful part of treatment,’ says Whorwell. ‘But if you’re stressed out before a race or a hard training session, that can aggravate IBS. Moderate running is usually fine for IBS and may even help it. If you have constipation, more vigorous exercise (faster or longer running) can be useful. If you have loose IBS it’s best avoided.’

As a runner, your digestive system may be particularly sensitive to the physical jolting of running, or you may be sensitive to the specialist drinks or food you’re taking on board to fuel your efforts. ‘Avoid products containing fructose or artificial sweeteners, known to cause upset,’ says Whorwell. ‘Adjust your meal timings and try self-hypnosis and meditation to calm nerves.’

Running has also been linked to ‘leaky gut syndrome’. ‘This is a controversial area but the condition does exist,’ says Whorwell. ‘The gut can become more permeable after an infection and let potentially harmful food antigens and bacteria into the bloodstream. This can also happen due to stress and, it’s thought, exercise - although only in the short term.

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Could probiotics be the answer?

Research published in the European Journal of Applied Physiology suggested taking probiotics – supplements containing live bacteria – not only reduced gut permeability but increased the time it took runners to fatigue when training in hot temperatures. Another, published in the British Journal of Sports Medicine, found distance runners given a probiotic supplement for a month reported less than half the number of days of respiratory symptoms than a control group. Other research has suggested that probiotics may help reduce inflammation, oxidative stress and gastrointestinal illness in active people. So they have an indirect rather than ergogenic effect.

However, many experts question whether probiotic supps can really offer a magic bullet to the guts – at least for now. The difficulty is knowing which strains of bacteria a pill or powder contains, and which your microbiome lacks, in what amounts, and if they can survive the journey to your gut.

‘Because everyone’s microbiome is unique, there’s no one-size-fits-all approach to supplementing,’ explains Spector. ‘In the future, we can expect bespoke probiotic medication and my goal is formulations to fight obesity or other diseases.’

For now, though? Save your money and concentrate on your diet first.

How can I boost my microbiome?

‘Whether you want to deal with digestive issues or low immunity, or simply get yourself in the best possible shape to run better, show your microbes some TLC – and the benefits will cascade from that,’ says Danaher. But how, precisely can you apply that TLC? I wrote The G Plan Diet with nutritionist Amanda Hamilton to give people a practical guide to reaping the benefits of all the latest gut-health research. We know a healthy microbiome is plentiful and varied, so how do we increase our own diversity? We devised a 21-day plan designed to boost your digestive system, increase the number and diversity of your gut microbes and guide you into better eating habits for life. Here are some guiding principles you can take from it:

Go for variety: Our bodies thrive on real food and diversity. Yet the Western diet, based around processed convenience food and drinks, is very limited. Many of us eat as few as six or seven meals on rotation and fail to get our five – or should that be 10? – a day of fruit and vegetables. Danaher says a common problem is runners following faddy diets and therefore cutting out foods their microbiome needs.

‘The surest route to an abundant and diverse microbiome is a diverse diet,’ Spector agrees: ‘Runners can be guilty of getting into certain, limited dietary habits they think work for them. Branching out and enjoying a much wider range of foods is a very good start.’

From a weight-loss/management perspective, research shows that dieters who eat a greater variety of healthy foods are more likely to lose weight and fat long term and less likely to develop metabolic syndrome (associated with type 2 diabetes and heart disease). So, choose a rainbow of fruit and veg, try new foods and flavours, and eat seasonally. Each time you prepare a meal, think, ‘What else could I add?’ Then up the diversity with some sprouted seeds, some extra veg, a side of pickles.

Choose unprocessed: Variety doesn’t mean extra wings with your delivery pizza. Processed foods, takeaways and ready meals do our guts no favours. Very often high in sugar, salt, trans or saturated fats, additives and preservatives, they’re also much lower on the nutritional scale than real foods. Refined, white starchy carbs such as white flour, bread, pasta and rice offer much less for the microbiome than their wholegrain alternatives. Avoid them and you automatically avoid foods such as pastries, cakes and biscuits. Sugar suppresses beneficial bacteria and can allow unhealthy microbes to take over. Artificial sweeteners are equally unhelpful to gut health.

‘I can see why runners go for the instant fix of glucose-based drinks, gels and bars,’ says Spector. ‘But trying to wean yourself off processed energy foods and drinks and onto real food for fuel will benefit your digestion, overall health and performance.’

Feed your gut: What you eat doesn’t just feed you, it feeds your microbes, too. Make sure your diet includes plenty of prebiotics. These are foods made up of a form of indigestible fibre. They end up in the large intestine, where they provide a feast for waiting microbes. Think of them as fertiliser that helps your friendly bacteria to grow. Fibrous fruit and vegetables are top sources, as are wholegrains, pulses, nuts and seeds. Whorwell does caution that some people with IBS need to follow a lower fibre diet without fermentable carbs. If you react to these sorts of foods, ask a dietitian about the FODMAPS diet, which avoids them.)

Get fermenting: Fermented food and drinks contain live bacteria and yeasts – probiotics that survive the digestive tract and help to increase the population and activity of the microbiome. There are many ways to enjoy fermented products and they’re becoming fashionable as the health benefits are more widely reported. Get your fill of natural yoghurt, kefir, fermented vegetables or pickles and kombucha. Even aged, unpastuerised cheese and red wine have their benefits.

The G Plan Diet by Amanda Hamilton and Hannah Ebelthite is out now, along with The G Plan app (iTunes). For £85 you can participate in Professor Spector’s British Gut Project, which gives you a basic overview of your microbiome (via a stool test).

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